1. Field of the Invention
The present invention relates to automated chemical processes, and more particularly, to monitoring of process efficiency as affected by reagent flow and reaction.
2. Description of Related Art
Automated chemical processors for processes such as DNA (nucleic acid) synthesis, peptide synthesis and peptide sequencing generally require a system of valves and interconnecting tubings to deliver a predetermined series of chemicals to a reactor in which a desired series of chemical reactions takes place. The chemistries of these processes are well known. DNA synthesis, for example, is described generally in U.S. Pat. No. 4,458,066 issued to Caruthers et al, entitled "Process for Preparing Polynucleotides", which is incorporated by reference herein. This process involves the linking of nucleotides, which are the basic building blocks for DNA, to construct a single-stranded oligonucleotide. One of several approaches in synthesizing DNA is the so-called solid-phase phosphoramidite method which generally involves the steps of deblocking, activation, coupling, capping and oxidation in each synthesis cycle to add a nucleotide to a strand anchored to a solid-phase support. In an automated DNA synthesis apparatus, typically a delivery system dispenses a number of chemical reagents in predetermined sequence in a cycle into a reaction column according to instructions from the system controller or computer. After the desired number of cycles are completed, the operator removes the reaction column from the automated system and performs additional chemical procedures to retrieve the synthesized DNA fragment from the reaction column. In executing the automated steps, a variety of undesirable conditions may arise which lead to reduced efficiency or premature termination of the desired chemical reactions. For example, one undesirable condition is deterioration of one or more sensitive chemicals such that they no longer react efficiently. Other conditions include partial blockage of delivery tubing such that the desired chemical reagents are delivered at a reduced rate, and the depletion of chemical reagent in a particular reagent reservoir.
It is desirable to detect the above-mentioned conditions when they occur and to stop the process so that the conditions may be corrected before proceeding further. In the past, operators of automated DNA synthesis apparatus have engaged in the practice of observing the effluent from the chemical reactor to ascertain that the reaction is proceeding efficiently and that all the desired chemicals are flowing properly. Reaction efficiency is typically judged by observing the intensity of a characteristic bright orange color in the effluent containing dimethoxytrityl ion at a particular step of the process known as the deblocking step. Flow rates are often judged by measuring the volume of effluent over a fixed interval of time. However, the requirement for an operator to monitor constantly the operation of an automated instrument defeats much of the objective of automation. Attempts have been made in the past to monitor the flow system. For example, Biosearch Corporation has employed optical detectors on the delivery tubes from individual reagent reservoirs to detect the absence of reagents in the tubes. Pharmacia Instruments/LKB has provided in its commercial DNA synthesizer an on-line colorimeter to monitor dimethoxytrityl ions effluent and to derive therefrom a measure of reaction efficiency. This instrument automatically shuts down if reaction efficiency falls below a predetermined threshold. For all these instruments, a separate detector is required for each monitoring function, which adds to the complexity and cost of the instrument.